Analysis of GLDS-120 from NASA GeneLab

This R markdown file was auto-generated by the iDEP website Using iDEP 0.91, originally by Steven

Ge SX, Son EW, Yao R: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 2018, 19(1):534. PMID:30567491

1. Read data

First we set up the working directory to where the files are saved.

 setwd('~/Documents/HTML_R/GLDS120')

R packages and iDEP core Functions. Users can also download the iDEP_core_functions.R file. Many R packages needs to be installed first. This may take hours. Each of these packages took years to develop.So be a patient thief. Sometimes dependencies needs to be installed manually. If you are using an older version of R, and having trouble with package installation, try un-install the current version of R, delete all folders and files (C:/Program Files/R/R-3.4.3), and reinstall from scratch.

 if(file.exists('iDEP_core_functions.R'))
    source('iDEP_core_functions.R') else 
    source('https://raw.githubusercontent.com/iDEP-SDSU/idep/master/shinyapps/idep/iDEP_core_functions.R') 

We are using the downloaded gene expression file where gene IDs has been converted to Ensembl gene IDs. This is because the ID conversion database is too large to download. You can use your original file if your file uses Ensembl ID, or you do not want to use the pathway files available in iDEP (or it is not available).

 inputFile <- 'GLDS120_Expression.csv'
 sampleInfoFile <- 'GLDS120_Sampleinfo.csv'
 gldsMetadataFile <- 'GLDS120_Metadata.csv'
 geneInfoFile <- 'Arabidopsis_thaliana__athaliana_eg_gene_GeneInfo.csv' #Gene symbols, location etc. 
 geneSetFile <- 'Arabidopsis_thaliana__athaliana_eg_gene.db'  # pathway database in SQL; can be GMT format 
 STRING10_speciesFile <- 'https://raw.githubusercontent.com/iDEP-SDSU/idep/master/shinyapps/idep/STRING10_species.csv' 

Parameters for reading data

 input_missingValue <- 'geneMedian' #Missing values imputation method
 input_dataFileFormat <- 1  #1- read counts, 2 FKPM/RPKM or DNA microarray
 input_minCounts <- 0.5 #Min counts
 input_NminSamples <- 1 #Minimum number of samples 
 input_countsLogStart <- 4  #Pseudo count for log CPM
 input_CountsTransform <- 1 #Methods for data transformation of counts. 1-EdgeR's logCPM 2-VST, 3-rlog 
readMetadata.out <- readMetadata(gldsMetadataFile)
library(knitr)   #  install if needed. for showing tables with kable
library(kableExtra)
kable( readMetadata.out ) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%")
Col0_GC_Alight_Rep1 Col0_GC_Alight_Rep2 Col0_GC_Alight_Rep3 Col0_GC_dark_Rep1 Col0_GC_dark_Rep2 Col0_GC_dark_Rep3 Ws_GC_Alight_Rep1 Ws_GC_Alight_Rep2 Ws_GC_Alight_Rep3 Ws_GC_dark_Rep1 Ws_GC_dark_Rep2 Ws_GC_dark_Rep3 Col0PhyD_GC_Alight_Rep1 Col0PhyD_GC_Alight_Rep2 Col0PhyD_GC_Alight_Rep3 Col0PhyD_GC_dark_Rep1 Col0PhyD_GC_dark_Rep2 Col0PhyD_GC_dark_Rep3 Col0_FLT_Alight_Rep1 Col0_FLT_Alight_Rep2 Col0_FLT_Alight_Rep3 Col0_FLT_dark_Rep1 Col0_FLT_dark_Rep2 Col0_FLT_dark_Rep3 Ws_FLT_Alight_Rep1 Ws_FLT_Alight_Rep2 Ws_FLT_Alight_Rep3 Ws_FLT_dark_Rep1 Ws_FLT_dark_Rep2 Ws_FLT_dark_Rep3 Col0PhyD_FLT_Alight_Rep1 Col0PhyD_FLT_Alight_Rep2 Col0PhyD_FLT_Alight_Rep3 Col0PhyD_FLT_dark_Rep1 Col0PhyD_FLT_dark_Rep2 Col0PhyD_FLT_dark_Rep3
Sample.LongId Atha.Col.0.root.GC.Alight.Rep1.GSM2493759.RNAseq.RNAseq Atha.Col.0.root.GC.Alight.Rep2.GSM2493760.RNAseq.RNAseq Atha.Col.0.root.GC.Alight.Rep3.GSM2493761.RNAseq.RNAseq Atha.Col.0.root.GC.dark.Rep1.GSM2493768.RNAseq.RNAseq Atha.Col.0.root.GC.dark.Rep2.GSM2493769.RNAseq.RNAseq Atha.Col.0.root.GC.dark.Rep3.GSM2493770.RNAseq.RNAseq Atha.Ws.root.GC.Alight.Rep1.GSM2493762.RNAseq.RNAseq Atha.Ws.root.GC.Alight.Rep2.GSM2493763.RNAseq.RNAseq Atha.Ws.root.GC.Alight.Rep3.GSM2493764.RNAseq.RNAseq Atha.Ws.root.GC.dark.Rep1.GSM2493771.RNAseq.RNAseq Atha.Ws.root.GC.dark.Rep2.GSM2493772.RNAseq.RNAseq Atha.Ws.root.GC.dark.Rep3.GSM2493773.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.Alight.Rep1.GSM2493765.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.Alight.Rep2.GSM2493766.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.Alight.Rep3.GSM2493767.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.dark.Rep1.GSM2493774.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.dark.Rep2.GSM2493775.RNAseq.RNAseq Atha.Col.0.PhyD.root.GC.dark.Rep3.GSM2493776.RNAseq.RNAseq Atha.Col.0.root.FLT.Alight.Rep1.GSM2493777.RNAseq.RNAseq Atha.Col.0.root.FLT.Alight.Rep2.GSM2493778.RNAseq.RNAseq Atha.Col.0.root.FLT.Alight.Rep3.GSM2493779.RNAseq.RNAseq Atha.Col.0.root.FLT.dark.Rep1.GSM2493786.RNAseq.RNAseq Atha.Col.0.root.FLT.dark.Rep2.GSM2493787.RNAseq.RNAseq Atha.Col.0.root.FLT.dark.Rep3.GSM2493788.RNAseq.RNAseq Atha.Ws.root.FLT.Alight.Rep1.GSM2493780.RNAseq.RNAseq Atha.Ws.root.FLT.Alight.Rep2.GSM2493781.RNAseq.RNAseq Atha.Ws.root.FLT.Alight.Rep3.GSM2493782.RNAseq.RNAseq Atha.Ws.root.FLT.dark.Rep1.GSM2493789.RNAseq.RNAseq Atha.Ws.root.FLT.dark.Rep2.GSM2493790.RNAseq.RNAseq Atha.Ws.root.FLT.dark.Rep3.GSM2493791.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.Alight.Rep1.GSM2493783.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.Alight.Rep2.GSM2493784.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.Alight.Rep3.GSM2493785.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.dark.Rep1.GSM2493792.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.dark.Rep2.GSM2493793.RNAseq.RNAseq Atha.Col.0.PhyD.root.FLT.dark.Rep3.GSM2493794.RNAseq.RNAseq
Sample.Id
Sample.Name Atha_Col-0_root_GC_Alight_Rep1_GSM2493759 Atha_Col-0_root_GC_Alight_Rep2_GSM2493760 Atha_Col-0_root_GC_Alight_Rep3_GSM2493761 Atha_Col-0_root_GC_dark_Rep1_GSM2493768 Atha_Col-0_root_GC_dark_Rep2_GSM2493769 Atha_Col-0_root_GC_dark_Rep3_GSM2493770 Atha_Ws_root_GC_Alight_Rep1_GSM2493762 Atha_Ws_root_GC_Alight_Rep2_GSM2493763 Atha_Ws_root_GC_Alight_Rep3_GSM2493764 Atha_Ws_root_GC_dark_Rep1_GSM2493771 Atha_Ws_root_GC_dark_Rep2_GSM2493772 Atha_Ws_root_GC_dark_Rep3_GSM2493773 Atha_Col-0-PhyD_root_GC_Alight_Rep1_GSM2493765 Atha_Col-0-PhyD_root_GC_Alight_Rep2_GSM2493766 Atha_Col-0-PhyD_root_GC_Alight_Rep3_GSM2493767 Atha_Col-0-PhyD_root_GC_dark_Rep1_GSM2493774 Atha_Col-0-PhyD_root_GC_dark_Rep2_GSM2493775 Atha_Col-0-PhyD_root_GC_dark_Rep3_GSM2493776 Atha_Col-0_root_FLT_Alight_Rep1_GSM2493777 Atha_Col-0_root_FLT_Alight_Rep2_GSM2493778 Atha_Col-0_root_FLT_Alight_Rep3_GSM2493779 Atha_Col-0_root_FLT_dark_Rep1_GSM2493786 Atha_Col-0_root_FLT_dark_Rep2_GSM2493787 Atha_Col-0_root_FLT_dark_Rep3_GSM2493788 Atha_Ws_root_FLT_Alight_Rep1_GSM2493780 Atha_Ws_root_FLT_Alight_Rep2_GSM2493781 Atha_Ws_root_FLT_Alight_Rep3_GSM2493782 Atha_Ws_root_FLT_dark_Rep1_GSM2493789 Atha_Ws_root_FLT_dark_Rep2_GSM2493790 Atha_Ws_root_FLT_dark_Rep3_GSM2493791 Atha_Col-0-PhyD_root_FLT_Alight_Rep1_GSM2493783 Atha_Col-0-PhyD_root_FLT_Alight_Rep2_GSM2493784 Atha_Col-0-PhyD_root_FLT_Alight_Rep3_GSM2493785 Atha_Col-0-PhyD_root_FLT_dark_Rep1_GSM2493792 Atha_Col-0-PhyD_root_FLT_dark_Rep2_GSM2493793 Atha_Col-0-PhyD_root_FLT_dark_Rep3_GSM2493794
GLDS 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120
Accession GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120 GLDS-120
Hardware Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish Petri dish
Tissue Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots Roots
Age 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days 11 days
Organism Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana
Ecotype Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 WS-0 WS-0 WS-0 WS-0 WS-0 WS-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0 WS-0 WS-0 WS-0 WS-0 WS-0 WS-0 Col-0 Col-0 Col-0 Col-0 Col-0 Col-0
Genotype WT WT WT WT WT WT WT WT WT WT WT WT PhyD PhyD PhyD PhyD PhyD PhyD WT WT WT WT WT WT WT WT WT WT WT WT PhyD PhyD PhyD PhyD PhyD PhyD
Variety Col-0 WT Col-0 WT Col-0 WT Col-0 WT Col-0 WT Col-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 WT Col-0 WT Col-0 WT Col-0 WT Col-0 WT Col-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT WS-0 WT Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD Col-0 PhyD
Radiation Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Background Earth Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation Cosmic radiation
Gravity Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Terrestrial Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity Microgravity
Developmental 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots 11 day old seedling roots
Time.series.or.Concentration.gradient Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point Single time point
Light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light 4-6 umoles m-2 s-1 total light Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown Light-activated for 4 hours, then dark-grown
Analysis.Light Alight Alight Alight Dark Dark Dark Alight Alight Alight Dark Dark Dark Alight Alight Alight Dark Dark Dark Alight Alight Alight Dark Dark Dark Alight Alight Alight Dark Dark Dark Alight Alight Alight Dark Dark Dark
Assay..RNAseq. RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling RNAseq Transcription Profiling
Temperature
Treatment.type
Treatment.intensity X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X
Treament.timing X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X
Preservation.Method. RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater RNAlater
 readData.out <- readData(inputFile) 
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
   kable( head(readData.out$data) ) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Col0_GC_Alight_Rep1 Col0_GC_Alight_Rep2 Col0_GC_Alight_Rep3 Col0_GC_dark_Rep1 Col0_GC_dark_Rep2 Col0_GC_dark_Rep3 Ws_GC_Alight_Rep1 Ws_GC_Alight_Rep2 Ws_GC_Alight_Rep3 Ws_GC_dark_Rep1 Ws_GC_dark_Rep2 Ws_GC_dark_Rep3 Col0PhyD_GC_Alight_Rep1 Col0PhyD_GC_Alight_Rep2 Col0PhyD_GC_Alight_Rep3 Col0PhyD_GC_dark_Rep1 Col0PhyD_GC_dark_Rep2 Col0PhyD_GC_dark_Rep3 Col0_FLT_Alight_Rep1 Col0_FLT_Alight_Rep2 Col0_FLT_Alight_Rep3 Col0_FLT_dark_Rep1 Col0_FLT_dark_Rep2 Col0_FLT_dark_Rep3 Ws_FLT_Alight_Rep1 Ws_FLT_Alight_Rep2 Ws_FLT_Alight_Rep3 Ws_FLT_dark_Rep1 Ws_FLT_dark_Rep2 Ws_FLT_dark_Rep3 Col0PhyD_FLT_Alight_Rep1 Col0PhyD_FLT_Alight_Rep2 Col0PhyD_FLT_Alight_Rep3 Col0PhyD_FLT_dark_Rep1 Col0PhyD_FLT_dark_Rep2 Col0PhyD_FLT_dark_Rep3
AT1G07590 14.09484 15.82643 16.00050 13.10404 13.51777 14.64386 13.409439 15.77315 14.82674 8.734572 12.853189 14.49060 14.30307 16.42429 16.25823 14.93434 14.023780 13.652232 13.06820 13.47644 15.85437 14.53257 12.546514 16.29378 13.70761 17.15691 15.84185 11.771773 15.17731 15.44411 15.63005 16.46416 16.53664 16.16638 14.22419 11.227882
AT1G21310 13.82237 12.89321 13.59194 12.69178 11.84638 13.57377 11.609280 14.87147 13.40320 10.803775 11.668910 12.93797 12.21651 15.52722 14.64023 14.21443 13.702426 13.487243 13.86935 13.89505 14.02481 14.15226 13.295761 15.67999 14.01774 15.40720 14.53493 13.029378 14.92947 14.70538 14.61414 13.92094 14.68044 14.58744 13.84959 11.987155
AT2G33830 13.00360 12.70793 13.19989 11.07625 11.44428 12.10500 11.605670 13.01332 13.23629 6.342765 8.041026 10.62547 13.12869 14.63728 13.86356 12.00093 9.571015 8.582187 13.84084 13.54377 14.43678 13.47765 11.086524 14.73928 13.32348 14.63064 13.90582 9.399696 12.33273 12.11427 14.45015 14.83492 14.74970 13.46973 13.62021 13.043726
AT1G07610 12.08104 14.30673 14.23944 10.40031 11.39977 12.30921 9.268934 12.67998 11.15489 4.495592 9.733672 10.63264 11.22988 14.58783 14.11140 12.85493 11.888352 11.502633 10.64115 11.46993 13.77730 12.79971 9.080162 14.60663 10.27736 13.91128 12.58584 8.510065 11.83719 12.25284 13.89512 14.26232 14.34338 13.98226 11.39071 6.943481
AT5G03240 13.20130 13.12291 13.32156 11.49666 11.57663 13.03192 12.702830 13.73541 14.16480 10.261950 10.374225 11.62274 13.07120 14.91590 14.53655 13.45543 11.608011 11.671690 12.73701 13.21551 13.74191 12.73065 10.975705 12.96365 12.31093 14.01545 13.06204 10.566490 12.53392 12.64681 13.26962 14.37130 14.68130 13.65752 12.14785 12.731019
AT2G45960 14.76921 14.16179 14.40573 12.98223 12.07059 13.29898 13.412024 14.52394 14.19108 11.907155 12.186793 12.66575 12.72364 15.00718 14.16692 13.92458 12.483819 12.222020 13.90170 13.63596 14.27782 13.88254 12.522675 13.61255 14.13872 13.88720 14.02430 11.971582 13.47262 13.65144 13.90907 13.79361 14.08793 13.30008 12.89654 12.072701
 readSampleInfo.out <- readSampleInfo(sampleInfoFile) 
 kable( readSampleInfo.out ) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Gravity Variety Light
Col0_GC_Alight_Rep1 Terrestrial Col0 WT Alight
Col0_GC_Alight_Rep2 Terrestrial Col0 WT Alight
Col0_GC_Alight_Rep3 Terrestrial Col0 WT Alight
Col0_GC_dark_Rep1 Terrestrial Col0 WT Dark
Col0_GC_dark_Rep2 Terrestrial Col0 WT Dark
Col0_GC_dark_Rep3 Terrestrial Col0 WT Dark
Ws_GC_Alight_Rep1 Terrestrial WS0 WT Alight
Ws_GC_Alight_Rep2 Terrestrial WS0 WT Alight
Ws_GC_Alight_Rep3 Terrestrial WS0 WT Alight
Ws_GC_dark_Rep1 Terrestrial WS0 WT Dark
Ws_GC_dark_Rep2 Terrestrial WS0 WT Dark
Ws_GC_dark_Rep3 Terrestrial WS0 WT Dark
Col0PhyD_GC_Alight_Rep1 Terrestrial Col0 PhyD Alight
Col0PhyD_GC_Alight_Rep2 Terrestrial Col0 PhyD Alight
Col0PhyD_GC_Alight_Rep3 Terrestrial Col0 PhyD Alight
Col0PhyD_GC_dark_Rep1 Terrestrial Col0 PhyD Dark
Col0PhyD_GC_dark_Rep2 Terrestrial Col0 PhyD Dark
Col0PhyD_GC_dark_Rep3 Terrestrial Col0 PhyD Dark
Col0_FLT_Alight_Rep1 Microgravity Col0 WT Alight
Col0_FLT_Alight_Rep2 Microgravity Col0 WT Alight
Col0_FLT_Alight_Rep3 Microgravity Col0 WT Alight
Col0_FLT_dark_Rep1 Microgravity Col0 WT Dark
Col0_FLT_dark_Rep2 Microgravity Col0 WT Dark
Col0_FLT_dark_Rep3 Microgravity Col0 WT Dark
Ws_FLT_Alight_Rep1 Microgravity WS0 WT Alight
Ws_FLT_Alight_Rep2 Microgravity WS0 WT Alight
Ws_FLT_Alight_Rep3 Microgravity WS0 WT Alight
Ws_FLT_dark_Rep1 Microgravity WS0 WT Dark
Ws_FLT_dark_Rep2 Microgravity WS0 WT Dark
Ws_FLT_dark_Rep3 Microgravity WS0 WT Dark
Col0PhyD_FLT_Alight_Rep1 Microgravity Col0 PhyD Alight
Col0PhyD_FLT_Alight_Rep2 Microgravity Col0 PhyD Alight
Col0PhyD_FLT_Alight_Rep3 Microgravity Col0 PhyD Alight
Col0PhyD_FLT_dark_Rep1 Microgravity Col0 PhyD Dark
Col0PhyD_FLT_dark_Rep2 Microgravity Col0 PhyD Dark
Col0PhyD_FLT_dark_Rep3 Microgravity Col0 PhyD Dark
 input_selectOrg ="NEW" 
 input_selectGO <- 'GOBP'   #Gene set category 
 input_noIDConversion = TRUE  
 allGeneInfo.out <- geneInfo(geneInfoFile) 
 converted.out = NULL 
 convertedData.out <- convertedData()    
 nGenesFilter()  
## [1] "16156 genes in 36 samples. 16155  genes passed filter.\n Original gene IDs used."
 convertedCounts.out <- convertedCounts()  # converted counts, just for compatibility 

2. Pre-process

# Read counts per library 
 parDefault = par() 
 par(mar=c(12,4,2,2)) 
 # barplot of total read counts
 x <- readData.out$rawCounts
 groups = as.factor( detectGroups(colnames(x ) ) )
 if(nlevels(groups)<=1 | nlevels(groups) >20 )  
  col1 = 'green'  else
  col1 = rainbow(nlevels(groups))[ groups ]             
         
 barplot( colSums(x)/1e6, 
        col=col1,las=3, main="Total read counts (millions)")  

 readCountsBias()  # detecting bias in sequencing depth 
## [1] 0.05123677
## [1] 0.5460606
## [1] 0.2013552
## [1] 0.3019591
## [1] "No bias detected"
 # Box plot 
 x = readData.out$data 
 boxplot(x, las = 2, col=col1,
    ylab='Transformed expression levels',
    main='Distribution of transformed data') 

 #Density plot 
 par(parDefault) 
## Warning in par(parDefault): graphical parameter "cin" cannot be set
## Warning in par(parDefault): graphical parameter "cra" cannot be set
## Warning in par(parDefault): graphical parameter "csi" cannot be set
## Warning in par(parDefault): graphical parameter "cxy" cannot be set
## Warning in par(parDefault): graphical parameter "din" cannot be set
## Warning in par(parDefault): graphical parameter "page" cannot be set
 densityPlot()       

 # Scatter plot of the first two samples 
 plot(x[,1:2],xlab=colnames(x)[1],ylab=colnames(x)[2], 
    main='Scatter plot of first two samples') 

 ####plot gene or gene family
 input_selectOrg ="BestMatch" 
 input_geneSearch <- 'HOXA' #Gene ID for searching 
 genePlot()  
## NULL
 input_useSD <- 'FALSE' #Use standard deviation instead of standard error in error bar? 
 geneBarPlotError()       
## NULL

3. Heatmap

 # hierarchical clustering tree
 x <- readData.out$data
 maxGene <- apply(x,1,max)
 # remove bottom 25% lowly expressed genes, which inflate the PPC
 x <- x[which(maxGene > quantile(maxGene)[1] ) ,] 
 plot(as.dendrogram(hclust2( dist2(t(x)))), ylab="1 - Pearson C.C.", type = "rectangle") 

 #Correlation matrix
 input_labelPCC <- TRUE #Show correlation coefficient? 
 correlationMatrix() 

 # Parameters for heatmap
 input_nGenes <- 1000   #Top genes for heatmap
 input_geneCentering <- TRUE    #centering genes ?
 input_sampleCentering <- FALSE #Center by sample?
 input_geneNormalize <- FALSE   #Normalize by gene?
 input_sampleNormalize <- FALSE #Normalize by sample?
 input_noSampleClustering <- FALSE  #Use original sample order
 input_heatmapCutoff <- 4   #Remove outliers beyond number of SDs 
 input_distFunctions <- 1   #which distant funciton to use
 input_hclustFunctions <- 1 #Linkage type
 input_heatColors1 <- 1 #Colors
 input_selectFactorsHeatmap <- 'Light'  #Sample coloring factors 
 png('heatmap.png', width = 10, height = 15, units = 'in', res = 300) 
 staticHeatmap() 
 dev.off()  
## png 
##   2

[heatmap] (heatmap.png)

 heatmapPlotly() # interactive heatmap using Plotly 

4. K-means clustering

 input_nGenesKNN <- 2000    #Number of genes fro k-Means
 input_nClusters <- 4   #Number of clusters 
 maxGeneClustering = 12000
 input_kmeansNormalization <- 'geneMean'    #Normalization
 input_KmeansReRun <- 0 #Random seed 

 distributionSD()  #Distribution of standard deviations 

 KmeansNclusters()  #Number of clusters 

 Kmeans.out = Kmeans()   #Running K-means 
 KmeansHeatmap()   #Heatmap for k-Means 

 #Read gene sets for enrichment analysis 
 sqlite  <- dbDriver('SQLite')
 input_selectGO3 <- 'GOBP'  #Gene set category
 input_minSetSize <- 15 #Min gene set size
 input_maxSetSize <- 2000   #Max gene set size 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO3,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  )  
 # Alternatively, users can use their own GMT files by
 #GeneSets.out <- readGMTRobust('somefile.GMT')  
 results <- KmeansGO()  #Enrichment analysis for k-Means clusters   
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Cluster adj.Pval Genes Pathways
A 2.25e-169 236 Amide biosynthetic process
7.51e-167 225 Translation
1.76e-166 225 Peptide biosynthetic process
2.01e-161 313 Organonitrogen compound biosynthetic process
2.03e-159 242 Cellular amide metabolic process
4.21e-158 226 Peptide metabolic process
1.69e-89 137 Ribonucleoprotein complex biogenesis
5.02e-83 206 Cellular component biogenesis
1.94e-71 109 Ribosome biogenesis
1.93e-62 95 Response to cadmium ion
B 1.41e-14 17 Detoxification
2.90e-14 19 Response to toxic substance
2.90e-14 16 Drug catabolic process
2.90e-14 15 Cellular oxidant detoxification
3.83e-14 10 Water transport
3.83e-14 10 Fluid transport
3.83e-14 15 Cellular detoxification
4.93e-14 12 Hydrogen peroxide catabolic process
7.79e-14 15 Cellular response to toxic substance
2.35e-13 20 Response to oxidative stress
C 1.83e-32 129 Response to abiotic stimulus
2.31e-31 83 Response to inorganic substance
4.80e-25 54 Response to metal ion
1.10e-23 88 Cellular catabolic process
4.30e-23 96 Catabolic process
5.18e-23 45 Response to cadmium ion
5.68e-22 93 Response to oxygen-containing compound
7.79e-21 87 Oxidation-reduction process
9.68e-21 88 Cellular response to chemical stimulus
6.58e-19 74 Response to acid chemical
D 1.66e-16 51 Response to abiotic stimulus
1.66e-16 20 Cellular response to decreased oxygen levels
1.66e-16 43 Cellular response to chemical stimulus
1.66e-16 20 Cellular response to oxygen levels
1.66e-16 20 Cellular response to hypoxia
7.26e-16 38 Cellular response to stress
9.22e-16 20 Response to hypoxia
1.07e-15 20 Response to decreased oxygen levels
1.07e-15 20 Response to oxygen levels
2.58e-15 39 Response to external stimulus
 input_seedTSNE <- 0    #Random seed for t-SNE
 input_colorGenes <- TRUE   #Color genes in t-SNE plot? 
 tSNEgenePlot()  #Plot genes using t-SNE 

5. PCA and beyond

 input_selectFactors <- 'Variety'   #Factor coded by color
 input_selectFactors2 <- 'Light'    #Factor coded by shape
 input_tsneSeed2 <- 0   #Random seed for t-SNE 
 #PCA, MDS and t-SNE plots
 PCAplot()  

 MDSplot() 

 tSNEplot()  

 #Read gene sets for pathway analysis using PGSEA on principal components 
 input_selectGO6 <- 'GOBP' 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO6,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  )  
 PCApathway() # Run PGSEA analysis 
## Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
##   version 3.12

 cat( PCA2factor() )   #The correlation between PCs with factors 
## 
##  Correlation between Principal Components (PCs) with factors
## PC1 is correlated with Light (p=5.73e-03).
## PC2 is correlated with Variety (p=2.38e-06).
## PC5 is correlated with Gravity (p=1.07e-05).

6. DEG1

 input_CountsDEGMethod <- 3 #DESeq2= 3,limma-voom=2,limma-trend=1 
 input_limmaPval <- 0.1 #FDR cutoff
 input_limmaFC <- 2 #Fold-change cutoff
 input_selectModelComprions <- 'Gravity: Microgravity vs. Terrestrial'  #Selected comparisons
 input_selectFactorsModel <- 'Gravity'  #Selected comparisons
 input_selectInteractions <- NULL   #Selected comparisons
 input_selectBlockFactorsModel <- NULL  #Selected comparisons
 factorReferenceLevels.out <- c('Gravity:Terrestrial','Light:Alight') 

 limma.out <- limma()
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
 DEG.data.out <- DEG.data()
 limma.out$comparisons 
## [1] "Microgravity-Terrestrial"
 input_selectComparisonsVenn = limma.out$comparisons[1:3] # use first three comparisons
 input_UpDownRegulated <- FALSE #Split up and down regulated genes 
 vennPlot() # Venn diagram 

  sigGeneStats() # number of DEGs as figure 

  sigGeneStatsTable() # number of DEGs as table 
##                                       Comparisons Up Down
## Microgravity-Terrestrial Microgravity-Terrestrial 77   50

7. DEG2

 input_selectContrast <- 'Microgravity-Terrestrial' #Selected comparisons 
 selectedHeatmap.data.out <- selectedHeatmap.data()
 selectedHeatmap()   # heatmap for DEGs in selected comparison
## $genes
##           Col0_GC_Alight_Rep1 Col0_GC_Alight_Rep2 Col0_GC_Alight_Rep3
## AT3G62040            8.104727           11.568320           11.697708
## AT5G05960            7.184797           10.242935           10.254254
## AT5G13930            9.633729            8.863853            9.079192
## AT2G21640            4.220106            5.369623            5.263637
## AT4G31910            8.778767            9.839191           10.017478
## AT3G03780            8.068476            7.514599            7.906864
## AT2G40900            8.348801            9.525778            9.824455
## AT2G41480            6.566055            9.736564            9.515016
## AT5G63850            6.624296            9.016747            9.247347
## AT3G54500            8.967762            8.413979            8.572169
## AT3G02850            7.184797            6.833750            7.084960
## AT5G37260            7.074229            7.992095            8.451734
## AT4G31730            7.094973            8.471031            8.703877
## AT3G23810            6.505365            7.857968            7.333875
## AT3G17609            8.031291            7.545284            7.598275
## AT3G26830            5.582295            6.676309            6.976491
## AT5G05270            7.602012            7.782703            7.717650
## AT2G46830            7.063744            7.213971            7.126162
## AT3G51240            7.895992            7.223490            6.965181
## AT3G09600            7.194441            7.756716            7.796338
## AT5G17300            7.241716            7.814542            8.175731
## AT5G47990            2.000000            2.987502            3.444032
## AT4G01440            2.573281            5.859255            6.369208
## AT4G09950            5.177983            5.225486            5.650070
## AT1G78580            6.624296            6.918234            6.484596
## AT5G50120            5.552608            7.052461            7.491961
## AT3G54820            4.060523            3.981213            4.734235
## AT5G44350            3.973583            5.677282            5.810333
## AT2G47560            2.000000            6.298089            7.185841
## AT3G57020            5.921170            5.531638            5.908068
## AT3G06020            2.000000            6.986908            6.298877
## AT5G08640            5.800066            5.065335            5.784828
## AT3G03770            4.494437            5.262893            4.439601
## AT2G25680            4.142520            3.568275            3.790058
## AT1G30380            4.555580            5.953783            5.758865
## AT3G56730            3.150403            6.185717            6.634906
## AT5G56720            4.060523            4.228145            4.372699
## AT5G64940            6.288384            5.976478            4.885877
## AT2G47460            5.098033            5.784058            5.678047
## AT2G02020            3.676072            3.683106            3.790058
## AT5G50800            2.000000            2.796649            3.156490
## AT4G24670            4.670600            4.372029            4.786574
## AT1G29910            5.360388            6.020824            4.503539
## AT1G11700            2.792319            5.369623            5.931501
## AT4G25830            4.494437            5.147632            5.650070
## AT4G15430            4.494437            4.679226            5.335664
## AT4G26790            3.973583            4.885159            3.568825
## AT1G68585            3.150403            4.438924            4.228798
## AT5G13630            3.973583            5.262893            3.981833
## AT1G62710            2.314931            4.301880            3.981833
## AT3G05880           11.327215           12.203435           11.984178
## AT3G44300           11.440452           11.115770           10.747271
## AT2G26400            5.582295            3.789468            5.023084
## AT3G54040            6.624296            9.213468            9.739051
## AT1G19960            8.318253            9.678921            9.112891
## AT5G23220            8.504212            7.845693            7.777065
## AT5G24530            7.847918            7.906048            8.402275
## AT5G22555            6.988136            7.418421            7.648631
## AT3G56400            7.184797            6.298089            7.009896
## AT5G05500            6.095994            7.975291            8.233434
## AT5G66170            6.872751            7.341832            6.591435
## AT1G56300            8.063223            7.459277            6.796771
## AT1G51420            7.658846            7.763257            7.620072
## AT5G01210            6.156451            5.704726            6.224941
## AT3G21510            6.032891            7.857968            8.406462
## AT5G66780            5.639896            3.443507            2.987914
## AT3G22121            7.323093            4.836365            6.809475
## AT5G07010            8.052657            7.041741            6.822067
## AT5G41280            6.075265            6.545817            6.147010
## AT5G13330            6.680276            6.084888            6.205850
## AT1G49720            7.287490            6.821266            7.289225
## AT3G22120            7.481150            4.564073            5.758865
## AT2G46680            6.095994            6.870564            6.515937
## AT5G15120            6.580837            4.068305            4.564763
## AT3G53160            7.890070            4.502855            4.372699
## AT2G18690            2.000000            4.932356            5.066066
## AT2G15960            4.876320            3.789468            4.439601
## AT3G17790            4.060523            4.885159            5.107804
## AT4G13195            7.063744            4.228145            5.107804
## AT5G02810            7.496823            6.084888            6.316784
## AT4G13390            3.150403            4.836365            5.370373
## AT2G44080            5.459697            5.500658            5.860028
## AT1G12040            3.973583            6.261596            6.106407
## AT1G22770            6.054234            6.368419            6.298877
## AT4G33070            6.442008            5.403514            5.107804
## AT3G52770            5.695286            5.930725            5.784828
## AT4G33980            4.827574            5.591671            5.226228
## AT2G43570            3.300833            5.468998            5.300100
## AT2G36470            4.430589            6.063847            5.732426
## AT1G06460            6.306284            4.502855            5.532397
## AT1G48930            4.614236            5.930725            5.148368
## AT5G48175            4.494437            5.953783            5.931501
## AT5G02230            3.676072            3.789468            4.228798
## AT1G11210            2.573281            5.187084            4.734235
## AT4G12290            5.459697            3.888524            4.228798
## AT5G18470            3.150403            3.789468            3.568825
## AT3G23150            5.253734            4.372029            3.889130
## AT5G57540            2.000000            2.987502            2.987914
## AT5G24470            5.290169            5.147632            4.439601
## AT5G61650            3.782207            3.568275            4.885877
## AT1G02450            2.982442            3.306918            2.987914
## AT5G19790            2.792319            5.976478            4.679927
## AT2G28690            4.777124            4.622798            4.439601
## AT2G05520            2.314931            2.576643            3.790058
## AT2G20520            2.000000            2.000000            3.444032
## AT5G42900            4.430589            4.301880            4.933077
## AT1G54970            2.000000            2.316942            3.156490
## AT5G22270            2.982442            3.789468            2.987914
## AT2G20560            4.555580            4.836365            5.148368
## AT1G28480            2.982442            3.156032            3.307413
## AT3G53800            5.325706            4.978058            4.933077
## AT5G61660            4.142520            3.888524            4.933077
## AT5G18270            3.300833            4.622798            4.885877
## AT3G10040            4.430589            3.981213            3.156490
## AT4G03440            4.555580            5.022356            4.933077
## AT3G04070            2.314931            3.306918            2.987914
## AT3G10710            2.000000            4.502855            3.444032
## AT1G79320            2.000000            3.789468            3.568825
## AT1G64480            2.000000            3.306918            2.987914
## AT3G05930            4.220106            4.068305            5.023084
## AT1G01660            3.300833            4.228145            3.790058
## AT5G25190            2.573281            3.683106            2.797002
## AT4G35180            2.000000            2.000000            2.000000
## AT1G16440            2.000000            3.981213            2.797002
## AT2G46860            2.000000            2.796649            2.576916
## AT1G25240            2.000000            2.316942            2.797002
## AT1G79860            2.314931            2.796649            2.000000
##           Ws_GC_Alight_Rep1 Ws_GC_Alight_Rep2 Ws_GC_Alight_Rep3
## AT3G62040          8.612741          8.041874          7.864678
## AT5G05960          7.580363          9.495186          7.621008
## AT5G13930          5.989479         10.560442          6.642980
## AT2G21640          5.138793          4.372448          4.674539
## AT4G31910          8.686364          8.575583          8.227133
## AT3G03780          5.825356          7.410616          7.834058
## AT2G40900          8.832511          8.150684          9.022141
## AT2G41480          6.324211          6.871066          7.169855
## AT5G63850          8.875117          7.846203          9.134463
## AT3G54500          8.710093          8.130581          8.305114
## AT3G02850          8.318510          8.435128          8.624284
## AT5G37260          7.602267          8.346402          8.357727
## AT4G31730          7.666051          6.717809          7.846384
## AT3G23810          5.611622          8.355091          7.711386
## AT3G17609          7.720473          7.987027          7.870725
## AT3G26830          5.216588          5.784540          3.679283
## AT5G05270          7.074482          8.337660          7.119960
## AT2G46830          7.779341          7.105406          7.649425
## AT3G51240          6.908597          8.068535          6.711965
## AT3G09600          7.213790          6.895098          7.236931
## AT5G17300          7.473503          6.704271          6.853033
## AT5G47990          2.792429          5.403984          2.574815
## AT4G01440          5.800308          4.068700          5.142704
## AT4G09950          6.375989          5.187546          6.525247
## AT1G78580          6.920270          6.546314          6.446465
## AT5G50120          4.969359          4.503283          5.878295
## AT3G54820          2.000000          4.503283          2.574815
## AT5G44350          4.923698          7.507332          2.984751
## AT2G47560          5.013619          4.679664          3.884471
## AT3G57020          4.293939          6.834251          4.927529
## AT3G06020          5.013619          3.156318          2.574815
## AT5G08640          4.876545          7.115670          5.102160
## AT3G03770          4.827798          4.679664          4.831589
## AT2G25680          3.437212          3.789837          3.152972
## AT1G30380          5.668097          5.999308          3.884471
## AT3G56730          3.561676          4.503283          3.679283
## AT5G56720          5.394492          3.156318          5.142704
## AT5G64940          6.270506          5.835105          5.556883
## AT2G47460          5.178215          6.262088          5.556883
## AT2G02020          3.973777          3.307227          2.000000
## AT5G50800          3.150546          2.796870          2.984751
## AT4G24670          4.614454          4.885608          5.644194
## AT1G29910          5.668097          4.372448          3.977066
## AT1G11700          4.614454          4.786308          2.984751
## AT4G25830          2.000000          5.107529          2.000000
## AT4G15430          4.220311          3.888903          5.220526
## AT4G26790          4.614454          3.443835          3.977066
## AT1G68585          2.982571          3.789837          4.223777
## AT5G13630          4.725066          3.888903          2.574815
## AT1G62710          4.827798          3.683464          3.679283
## AT3G05880         10.871893         11.963414         11.914083
## AT3G44300         10.834598         10.480302         11.042870
## AT2G26400          6.033136          5.954268          7.809085
## AT3G54040          6.136824          8.662156          8.109331
## AT1G19960          7.937038          9.779657          8.617107
## AT5G23220          7.727134          8.864367          8.700951
## AT5G24530          6.721130          8.020185          8.453502
## AT5G22555          3.437212          8.644544          7.099508
## AT3G56400          6.033136          7.669381          6.725375
## AT5G05500          2.314982          8.665653          4.674539
## AT5G66170          7.375155          7.242845          7.387917
## AT1G56300          6.195639          6.676808          6.256330
## AT1G51420          6.011473          7.802400          7.731462
## AT5G01210          5.800308          6.605773          6.628778
## AT3G21510          5.695526          7.583254          6.901093
## AT5G66780          4.494651          3.789837          4.618146
## AT3G22121          7.602267          6.846627          7.516897
## AT5G07010          6.908597          6.419498          7.169855
## AT5G41280          6.096239          7.821336          7.997721
## AT5G13330          5.098263          7.020560          7.697845
## AT1G49720          6.233558          6.690605          7.777248
## AT3G22120          7.543101          7.315877          7.846384
## AT2G46680          6.341678          6.744509          6.670971
## AT5G15120          4.494651          5.931210          6.292817
## AT3G53160          6.786364          5.954268          6.642980
## AT2G18690          3.150546          5.107529          2.984751
## AT2G15960          4.363992          5.187546          6.397045
## AT3G17790          3.782391          5.263358          5.182140
## AT4G13195          5.944461          5.469470          6.079660
## AT5G02810          6.721130          5.784540          6.363132
## AT4G13390          2.000000          2.796870          2.794295
## AT2G44080          5.013619          7.185538          5.925534
## AT1G12040          2.314982          5.883958          3.152972
## AT1G22770          6.931848          4.978511          6.100393
## AT4G33070          5.800308          5.501131          5.971275
## AT3G52770          4.876545          5.107529          5.142704
## AT4G33980          3.676251          6.085376          5.854082
## AT2G43570          2.314982          4.932807          3.679283
## AT2G36470          3.150546          5.562442          5.102160
## AT1G06460          4.670820          4.503283          5.672161
## AT1G48930          2.314982          5.677761          3.152972
## AT5G48175          3.676251          5.065792          5.398484
## AT5G02230          2.000000          4.978511          4.064076
## AT1G11210          2.982571          4.786308          3.152972
## AT4G12290          5.552846          4.439348          5.495594
## AT5G18470          3.881255          5.403984          3.439996
## AT3G23150          2.792429          4.228553          5.294364
## AT5G57540          2.000000          2.000000          2.000000
## AT5G24470          5.459934          5.621253          6.446465
## AT5G61650          2.573366          4.439348          3.679283
## AT1G02450          2.573366          3.888903          3.564595
## AT5G19790          2.792429          5.022811          2.984751
## AT2G28690          2.000000          3.789837          2.984751
## AT2G05520          2.314982          2.796870          2.000000
## AT2G20520          2.000000          2.000000          2.000000
## AT5G42900          3.973777          4.150840          4.297452
## AT1G54970          2.000000          2.000000          2.000000
## AT5G22270          2.000000          3.307227          2.574815
## AT2G20560          4.725066          4.302294          4.434395
## AT1G28480          3.300988          4.733971          2.574815
## AT3G53800          3.561676          5.107529          4.297452
## AT5G61660          2.573366          4.372448          4.434395
## AT5G18270          2.792429          4.302294          4.146135
## AT3G10040          3.782391          2.987760          3.679283
## AT4G03440          4.060721          5.022811          4.297452
## AT3G04070          3.676251          2.000000          4.880356
## AT3G10710          2.000000          2.796870          2.000000
## AT1G79320          2.000000          5.065792          2.000000
## AT1G64480          2.573366          4.623233          3.679283
## AT3G05930          3.881255          5.225950          4.064076
## AT1G01660          3.782391          4.439348          4.367548
## AT5G25190          2.314982          2.796870          2.574815
## AT4G35180          3.973777          3.307227          3.439996
## AT1G16440          2.314982          2.000000          2.000000
## AT2G46860          2.000000          2.000000          2.000000
## AT1G25240          2.792429          2.576814          2.000000
## AT1G79860          2.000000          2.000000          2.000000
##           Col0PhyD_GC_Alight_Rep1 Col0PhyD_GC_Alight_Rep2
## AT3G62040                9.330313                7.396435
## AT5G05960                9.144908                6.563949
## AT5G13930                2.000000                9.057714
## AT2G21640                5.299274                3.157781
## AT4G31910                9.255741                8.268367
## AT3G03780                8.678954                6.733772
## AT2G40900                7.917734                8.650708
## AT2G41480                7.935217                6.354170
## AT5G63850                7.084068                6.066828
## AT3G54500                6.730635                9.170510
## AT3G02850                7.251587                7.746656
## AT5G37260                8.297052                7.344924
## AT4G31730                7.155417                6.897659
## AT3G23810                7.633521                7.188116
## AT3G17609                3.306865                7.600566
## AT3G26830                6.952893                4.070720
## AT5G05270                5.022278                6.405358
## AT2G46830                4.885082                7.362299
## AT3G51240                2.000000                6.470901
## AT3G09600                7.223403                7.657977
## AT5G17300                6.676224                7.118244
## AT5G47990                4.502782                3.685290
## AT4G01440                7.675735                4.152894
## AT4G09950                6.757090                7.600566
## AT1G78580                5.591590                4.441510
## AT5G50120                6.368334                5.406385
## AT3G54820                5.369542                3.570377
## AT5G44350                5.225407                6.679355
## AT2G47560                2.000000                2.317568
## AT3G57020                3.306865                6.693153
## AT3G06020                4.563999                2.317568
## AT5G08640                2.000000                4.566707
## AT3G03770                4.836289                4.887900
## AT2G25680                2.796612                3.570377
## AT1G30380                3.443450                6.720359
## AT3G56730                4.932279                3.983581
## AT5G56720                5.369542                6.354170
## AT5G64940                2.796612                5.837570
## AT2G47460                2.000000                5.956748
## AT2G02020                5.907210                5.025136
## AT5G50800                2.000000                2.000000
## AT4G24670                4.502782                4.980826
## AT1G29910                3.683045                5.439505
## AT1G11700                4.733454                4.304407
## AT4G25830                2.000000                4.980826
## AT4G15430                3.981146                5.265733
## AT4G26790                4.438852                4.505466
## AT1G68585                3.306865                4.625454
## AT5G13630                2.000000                4.681902
## AT1G62710                4.502782                4.736224
## AT3G05880               11.302960               12.551491
## AT3G44300                9.699441               10.824388
## AT2G26400                7.483160                7.001113
## AT3G54040                7.393254                9.594727
## AT1G19960                7.851756               10.250767
## AT5G23220                7.393254                8.845534
## AT5G24530                7.073581                9.431463
## AT5G22555                3.306865                8.978238
## AT3G56400                7.145437                9.398155
## AT5G05500                4.371957                8.792043
## AT5G66170                7.736826                8.295756
## AT1G56300                6.402253                8.357710
## AT1G51420                6.833664                8.555726
## AT5G01210                6.952893                7.012163
## AT3G21510                6.530477                8.211979
## AT5G66780                3.306865                4.625454
## AT3G22121                5.187005                7.138555
## AT5G07010                7.084068                8.231021
## AT5G41280                5.731575                7.486346
## AT5G13330                7.125269                7.798636
## AT1G49720                7.213884                7.370909
## AT3G22120                6.204980                7.327336
## AT2G46680                6.619679                7.087231
## AT5G15120                7.801803                7.772880
## AT3G53160                6.929823                7.107980
## AT2G18690                5.334836                7.867182
## AT2G15960                6.385393                6.246000
## AT3G17790                5.147553                6.087871
## AT4G13195                6.648228                7.273250
## AT5G02810                5.859172                8.039093
## AT4G13390                4.150368                6.989978
## AT2G44080                6.605190                7.370909
## AT1G12040                4.885082                6.978756
## AT1G22770                5.561885                7.023129
## AT4G33070                5.731575                6.188713
## AT3G52770                4.371957                6.129058
## AT4G33980                4.885082                6.578890
## AT2G43570                4.228075                5.761032
## AT2G36470                5.299274                6.747061
## AT1G06460                5.262813                6.371435
## AT1G48930                3.683045                6.336696
## AT5G48175                4.977980                6.354170
## AT5G02230                3.155983                5.189907
## AT1G11210                3.683045                6.246000
## AT4G12290                4.371957                6.169101
## AT5G18470                3.306865                4.625454
## AT3G23150                6.105541                6.188713
## AT5G57540                2.796612                3.890838
## AT5G24470                4.679151                4.566707
## AT5G61650                3.306865                5.837570
## AT1G02450                2.316924                2.797995
## AT5G19790                2.316924                5.302202
## AT2G28690                3.443450                4.788575
## AT2G05520                5.299274                4.230639
## AT2G20520                2.316924                2.000000
## AT5G42900                4.563999                5.503548
## AT1G54970                2.000000                2.000000
## AT5G22270                4.977980                4.304407
## AT2G20560                4.228075                5.707653
## AT1G28480                2.000000                6.608315
## AT3G53800                5.591590                5.109873
## AT5G61660                2.000000                5.439505
## AT5G18270                4.885082                5.228318
## AT3G10040                6.166023                3.791722
## AT4G03440                4.679151                4.230639
## AT3G04070                4.622723                3.791722
## AT3G10710                2.316924                4.304407
## AT1G79320                2.796612                3.308808
## AT1G64480                2.000000                2.577688
## AT3G05930                3.981146                4.304407
## AT1G01660                3.443450                3.308808
## AT5G25190                3.981146                2.000000
## AT4G35180                2.000000                2.000000
## AT1G16440                2.796612                2.797995
## AT2G46860                2.796612                2.317568
## AT1G25240                2.796612                2.000000
## AT1G79860                2.000000                2.000000
##           Col0PhyD_GC_Alight_Rep3 Col0_FLT_Alight_Rep1 Col0_FLT_Alight_Rep2
## AT3G62040                9.894806             7.136576             6.996681
## AT5G05960               10.000006             4.486833             5.797668
## AT5G13930                9.251930             2.000000             2.314424
## AT2G21640                4.507339             4.135370             3.971658
## AT4G31910                8.946281             8.566906             8.713985
## AT3G03780                6.899856             6.827330             7.029320
## AT2G40900                9.425467             6.315177             7.112914
## AT2G41480                6.595856             3.874333             4.966879
## AT5G63850                8.595251             7.415879             7.229869
## AT3G54500                9.008396             6.297503             6.650077
## AT3G02850                8.983308             5.935570             7.040038
## AT5G37260                8.595251             4.915445             5.692902
## AT4G31730                8.406834             5.740067             5.772181
## AT3G23810                6.911725             6.243141             6.390135
## AT3G17609                8.209421             3.295345             3.559797
## AT3G26830                6.025932             4.486833             4.492313
## AT5G05270                7.302762             4.769227             5.095752
## AT2G46830                8.046723             3.295345             2.791227
## AT3G51240                7.256974             2.977881             2.314424
## AT3G09600                7.905477             3.966694             4.612075
## AT5G17300                7.519923             4.356334             3.879184
## AT5G47990                4.841048             2.000000             3.435419
## AT4G01440                5.536611             3.874333             5.918758
## AT4G09950                6.722546             5.352042             5.871534
## AT1G78580                6.722546             6.224555             5.822713
## AT5G50120                6.923497             4.769227             4.612075
## AT3G54820                2.990203             2.000000             4.291676
## AT5G44350                5.958875             3.145328             4.140522
## AT2G47560                6.303256             2.313121             2.314424
## AT3G57020                6.131201             4.356334             2.791227
## AT3G06020                4.982811             2.000000             2.000000
## AT5G08640                5.191931             2.788417             2.000000
## AT3G03770                4.790519             3.775652             4.722653
## AT2G25680                3.985279             2.977881             4.058559
## AT1G30380                6.248153             2.570255             2.981167
## AT3G56730                5.981575             2.788417             2.791227
## AT5G56720                3.793339             3.295345             3.879184
## AT5G64940                5.682300             3.145328             4.361702
## AT2G47460                6.151363             2.570255             2.791227
## AT2G02020                5.958875             4.212847             3.879184
## AT5G50800                4.376422             2.000000             2.000000
## AT4G24670                5.374540             4.547908             4.722653
## AT1G29910                4.507339             2.000000             3.435419
## AT1G11700                5.596664             2.788417             3.435419
## AT4G25830                5.267770             2.570255             2.572435
## AT4G15430                4.841048             3.431221             3.559797
## AT4G26790                4.072452             3.669723             2.572435
## AT1G68585                5.441569             2.570255             2.791227
## AT5G13630                5.152462             2.313121             2.572435
## AT1G62710                3.892499             2.570255             3.435419
## AT3G05880               12.235679            11.412351            11.785893
## AT3G44300               10.474249            12.045572            11.398331
## AT2G26400                5.596664             8.850617             9.217365
## AT3G54040                9.593308             6.671388             8.397157
## AT1G19960                9.439883             8.427604             8.848106
## AT5G23220                7.715420            10.195167            10.163114
## AT5G24530                8.937600             8.514319             8.599096
## AT5G22555                7.980648             8.606921             8.602715
## AT3G56400                7.715420             7.750650             8.205766
## AT5G05500                6.875822             7.649780             8.627799
## AT5G66170                6.667608             8.369577             7.355317
## AT1G56300                6.839002             8.610504             8.266352
## AT1G51420                7.456517             8.798163             8.454365
## AT5G01210                7.869416             6.956833             8.350561
## AT3G21510                7.881537             7.456265             7.724344
## AT5G66780                2.990203             5.602892             5.391919
## AT3G22121                7.646065             7.571052             8.388796
## AT5G07010                7.311747             8.621200             8.132543
## AT5G41280                6.958247             8.378011             7.690730
## AT5G13330                6.639334             7.763582             7.795649
## AT1G49720                7.440220             8.431661             8.652455
## AT3G22120                7.320677             7.348813             7.494297
## AT2G46680                6.489003             6.279609             6.321510
## AT5G15120                5.111882             6.511933             6.373283
## AT3G53160                5.152462             7.464208             7.509801
## AT2G18690                5.839684             6.685046             5.895339
## AT2G15960                5.267770             6.066565             5.425005
## AT3G17790                5.111882             5.791482             5.550245
## AT4G13195                6.722546             7.832706             7.968307
## AT5G02810                7.130643             7.391093             7.826930
## AT4G13390                3.159035             5.544149             7.462780
## AT2G44080                5.339821             7.022859             6.846030
## AT1G12040                4.507339             6.024208             7.248472
## AT1G22770                5.912374             7.731032             7.776549
## AT4G33070                6.068966             7.251192             6.882218
## AT3G52770                5.536611             5.208104             4.553436
## AT4G33980                5.935812             5.958246             6.093562
## AT2G43570                5.709752             4.769227             4.612075
## AT2G36470                6.303256             5.317381             6.303831
## AT1G06460                5.789107             6.629618             6.321510
## AT1G48930                4.790519             4.769227             6.212033
## AT5G48175                5.566950             6.107714             6.192951
## AT5G02230                4.683821             4.769227             4.361702
## AT1G11210                4.841048             5.245457             3.674297
## AT4G12290                5.596664             6.465202             6.321510
## AT5G18470                3.446951             5.317381             6.249456
## AT3G23150                4.376422             6.814960             6.963285
## AT5G57540                2.000000             2.000000             5.550245
## AT5G24470                5.763137             6.433185             6.548647
## AT5G61650                4.306221             4.053496             5.847330
## AT1G02450                3.571885             3.669723             4.058559
## AT5G19790                3.686857             4.212847             6.212033
## AT2G28690                4.232428             5.451291             5.692902
## AT2G05520                3.892499             4.053496             4.140522
## AT2G20520                2.000000             2.000000             5.941802
## AT5G42900                5.152462             5.602892             5.214051
## AT1G54970                2.000000             2.788417             5.579927
## AT5G22270                2.990203             3.555395             4.428485
## AT2G20560                4.376422             3.775652             4.361702
## AT1G28480                2.578438             2.570255             2.572435
## AT3G53800                5.191931             6.433185             6.051806
## AT5G61660                4.232428             3.775652             4.966879
## AT5G18270                5.736692             4.053496             5.579927
## AT3G10040                4.738156             4.868333             5.519940
## AT4G03440                5.267770             5.865324             5.609011
## AT3G04070                3.446951             4.486833             4.428485
## AT3G10710                2.318017             2.788417             6.249456
## AT1G79320                4.443365             4.716998             3.559797
## AT1G64480                3.793339             2.000000             2.981167
## AT3G05930                3.793339             4.053496             3.780375
## AT1G01660                2.990203             4.053496             3.148984
## AT5G25190                2.000000             4.135370             3.559797
## AT4G35180                2.000000             2.977881             3.559797
## AT1G16440                2.990203             2.977881             4.966879
## AT2G46860                2.000000             2.313121             2.572435
## AT1G25240                2.000000             2.000000             3.879184
## AT1G79860                2.000000             2.000000             2.981167
##           Col0_FLT_Alight_Rep3 Ws_FLT_Alight_Rep1 Ws_FLT_Alight_Rep2
## AT3G62040             5.137538           6.196179           7.756117
## AT5G05960             6.883597           6.342221           7.307486
## AT5G13930             2.000000           2.000000           2.000000
## AT2G21640             4.723864           5.098768           5.039530
## AT4G31910             7.154349           7.166122           6.901539
## AT3G03780             7.725745           7.233193           6.971920
## AT2G40900             8.113780           6.596266           7.971832
## AT2G41480             4.875322           5.057064           6.708921
## AT5G63850             6.719768           6.748128           8.256631
## AT3G54500             6.094906           6.681075           7.134173
## AT3G02850             7.259075           5.749396           6.223578
## AT5G37260             6.115340           6.215264           6.144523
## AT4G31730             6.155361           6.157236           7.715668
## AT3G23810             6.408154           5.553369           5.124381
## AT3G17609             3.781387           5.178723           5.609626
## AT3G26830             5.252700           2.000000           4.243559
## AT5G05270             5.773505           4.364452           6.223578
## AT2G46830             4.292813           5.139299           3.995850
## AT3G51240             3.560741           2.982853           2.000000
## AT3G09600             5.215325           4.969858           3.455911
## AT5G17300             4.493487           4.143163           3.166852
## AT5G47990             2.981872           2.000000           2.000000
## AT4G01440             4.219199           3.150860           4.695757
## AT4G09950             3.436320           4.924194           3.803403
## AT1G78580             3.880224           4.143163           5.972096
## AT5G50120             3.781387           3.881671           4.995157
## AT3G54820             2.791830           3.437572           3.995850
## AT5G44350             5.798994           3.881671           3.166852
## AT2G47560             2.314704           2.573554           2.583119
## AT3G57020             2.791830           3.150860           2.000000
## AT3G06020             2.314704           2.315094           2.000000
## AT5G08640             2.000000           2.000000           2.583119
## AT3G03770             4.429647           4.061155           3.803403
## AT2G25680             3.300147           3.150860           3.581274
## AT1G30380             3.560741           3.676643           3.455911
## AT3G56730             3.675278           2.000000           3.455911
## AT5G56720             3.300147           2.982853           2.583119
## AT5G64940             2.572902           4.220759           2.000000
## AT2G47460             3.300147           2.315094           3.581274
## AT2G02020             2.791830           2.000000           2.000000
## AT5G50800             2.000000           2.000000           3.581274
## AT4G24670             3.436320           3.881671           2.583119
## AT1G29910             2.981872           3.676643           3.318609
## AT1G11700             2.791830           2.982853           5.082579
## AT4G25830             2.572902           2.000000           2.583119
## AT4G15430             3.436320           2.000000           2.320823
## AT4G26790             3.300147           2.792670           2.997235
## AT1G68585             3.436320           2.315094           4.243559
## AT5G13630             2.572902           2.573554           2.000000
## AT1G62710             2.572902           3.301327           3.995850
## AT3G05880            12.943849          12.092880          13.852058
## AT3G44300            11.511421          11.963066          10.585065
## AT2G26400             8.780824          10.331928           9.719004
## AT3G54040            10.173091           8.185137          11.521948
## AT1G19960            10.193656           9.379332          11.221487
## AT5G23220            10.069555          10.415780           9.447766
## AT5G24530            10.132313           8.620482           9.545240
## AT5G22555             8.946798           9.707130          10.199054
## AT3G56400             9.864534           7.971667           8.256631
## AT5G05500             8.909256           9.383556           9.964592
## AT5G66170             9.048593           8.641798           9.184326
## AT1G56300             8.994463           7.971667           7.814741
## AT1G51420             8.784019           8.375301           7.251997
## AT5G01210             8.891594           7.551189           8.756066
## AT3G21510             8.173465           8.524291           9.358632
## AT5G66780             4.292813           5.722971           3.318609
## AT3G22121             6.975885           8.740605           9.194174
## AT5G07010             9.156058           7.010951           6.437662
## AT5G41280             7.952779           9.128135           8.429156
## AT5G13330             8.381797           8.287864           7.858745
## AT1G49720             8.712049           8.175425           8.408157
## AT3G22120             7.657714           8.524291           8.840002
## AT2G46680             9.246838           6.324754           7.701929
## AT5G15120             7.339442           5.395009           8.742708
## AT3G53160             7.924108           6.909149           6.533861
## AT2G18690             8.299361           7.350040           5.387309
## AT2G15960             7.083517           6.734965           7.988904
## AT3G17790             7.114300           5.217098           8.886294
## AT4G13195             6.733053           6.812204           6.609400
## AT5G02810             7.952779           7.588260           7.695010
## AT4G13390             5.920091           5.553369           6.594605
## AT2G44080             7.313147           7.489820           8.270660
## AT1G12040             6.964667           6.920822           7.412446
## AT1G22770             7.894856           6.490579           7.039026
## AT4G33070             7.083517           7.126347           7.971832
## AT3G52770             5.097013           5.139299           6.387045
## AT4G33980             7.705670           6.521573           7.960337
## AT2G43570             7.083517           4.143163           6.352286
## AT2G36470             7.144441           5.460453           7.103149
## AT1G06460             6.759260           5.800838           5.949018
## AT1G48930             6.679165           6.474828           7.478404
## AT5G48175             6.930479           6.458904           6.749557
## AT5G02230             6.594362           4.924194           4.243559
## AT1G11210             6.930479           2.792670           6.280150
## AT4G12290             6.733053           5.967680           5.827743
## AT5G18470             5.747557           5.428102           6.223578
## AT3G23150             6.975885           5.944995           6.695117
## AT5G57540             3.972721           4.828289           4.580350
## AT5G24470             6.269163           6.289172           5.352557
## AT5G61650             5.638833           5.553369           4.949376
## AT1G02450             4.776137           6.176839           5.242975
## AT5G19790             4.723864           5.850508           6.404116
## AT2G28690             6.608846           5.696053           6.060884
## AT2G05520             4.669626           2.000000           2.000000
## AT2G20520             4.362852           2.000000           2.000000
## AT5G42900             6.975885           5.696053           5.877483
## AT1G54970             4.292813           4.431266           2.000000
## AT5G22270             5.521243           4.431266           6.387045
## AT2G20560             5.359345           4.220759           6.827548
## AT1G28480             6.472931           4.364452           3.166852
## AT3G53800             5.012379           5.553369           5.609626
## AT5G61660             5.943137           5.057064           4.902094
## AT5G18270             5.824040           5.850508           5.667324
## AT3G10040             5.176956           4.969858           6.652895
## AT4G03440             5.798994           6.033672           5.387309
## AT3G04070             5.773505           4.364452           6.082253
## AT3G10710             5.426300           3.676643           4.387837
## AT1G79320             4.219199           5.326454           5.486810
## AT1G64480             3.675278           3.782796           5.802215
## AT3G05930             5.012379           4.614932           5.609626
## AT1G01660             5.176956           4.924194           5.722803
## AT5G25190             3.300147           3.974202           5.124381
## AT4G35180             2.000000           4.828289           3.318609
## AT1G16440             3.560741           4.431266           4.083231
## AT2G46860             2.314704           4.061155           3.166852
## AT1G25240             3.149768           3.437572           2.320823
## AT1G79860             3.972721           2.982853           2.320823
##           Ws_FLT_Alight_Rep3 Col0PhyD_FLT_Alight_Rep1 Col0PhyD_FLT_Alight_Rep2
## AT3G62040           7.031744                 6.163084                 6.702935
## AT5G05960           7.053267                 8.740140                 6.881790
## AT5G13930           2.000000                 2.000000                 2.000000
## AT2G21640           4.933077                 4.833612                 4.563350
## AT4G31910           6.809475                 7.448069                 7.008249
## AT3G03780           7.270970                 7.439945                 7.349696
## AT2G40900           7.435714                 7.579610                 7.417571
## AT2G41480           6.205850                 5.104240                 5.833813
## AT5G63850           7.351355                 8.338362                 6.986065
## AT3G54500           6.634907                 5.927733                 7.030096
## AT3G02850           6.224941                 7.398623                 8.007849
## AT5G37260           6.531356                 6.527499                 5.929912
## AT4G31730           6.834551                 6.258561                 6.401509
## AT3G23810           5.860028                 5.588735                 5.975663
## AT3G17609           4.885877                 4.676525                 4.438215
## AT3G26830           2.000000                 4.369446                 3.155553
## AT5G05270           4.734235                 5.400615                 4.149763
## AT2G46830           3.307413                 4.147957                 4.502139
## AT3G51240           2.987914                 2.985916                 3.887889
## AT3G09600           4.734235                 4.299328                 5.368837
## AT5G17300           5.226228                 5.296478                 4.732791
## AT5G47990           2.576916                 2.000000                 2.576356
## AT4G01440           3.568825                 5.856274                 3.155553
## AT4G09950           5.107804                 5.646359                 4.227460
## AT1G78580           2.797002                 5.433722                 4.884407
## AT5G50120           2.987914                 4.500219                 2.576356
## AT3G54820           4.503539                 3.886187                 2.796280
## AT5G44350           4.623494                 3.978823                 3.306400
## AT2G47560           3.156490                 2.575589                 2.576356
## AT3G57020           3.981833                 2.575589                 2.987071
## AT3G06020           2.000000                 2.316311                 2.000000
## AT5G08640           2.000000                 2.316311                 2.000000
## AT3G03770           4.228798                 4.369446                 3.980563
## AT2G25680           2.987914                 3.305011                 2.796280
## AT1G30380           4.151081                 3.566154                 3.442957
## AT3G56730           3.568825                 3.154268                 4.732791
## AT5G56720           3.981833                 5.332032                 2.987071
## AT5G64940           4.439602                 4.436314                 3.980563
## AT2G47460           3.307413                 3.566154                 2.576356
## AT2G02020           3.156490                 2.985916                 3.442957
## AT5G50800           3.156490                 2.000000                 2.316770
## AT4G24670           2.797002                 3.441483                 3.442957
## AT1G29910           3.568825                 2.316311                 2.576356
## AT1G11700           3.683678                 3.978823                 3.682507
## AT4G25830           2.576916                 2.316311                 2.987071
## AT4G15430           2.317106                 3.566154                 2.987071
## AT4G26790           3.790058                 3.305011                 4.067642
## AT1G68585           3.683678                 2.985916                 2.316770
## AT5G13630           2.317106                 2.316311                 2.796280
## AT1G62710           3.307413                 3.441483                 2.796280
## AT3G05880          12.888441                12.673667                13.054522
## AT3G44300          11.557900                11.561850                11.952405
## AT2G26400          10.168102                10.457603                 9.926873
## AT3G54040          10.376678                 9.790403                10.894433
## AT1G19960          10.373473                10.728316                10.674528
## AT5G23220          10.065928                 9.905501                 9.557245
## AT5G24530           8.918439                 9.679190                10.408730
## AT5G22555           9.912464                 9.178902                 7.781848
## AT3G56400           8.530575                 9.254966                 9.284803
## AT5G05500           9.597902                 7.885058                 7.963123
## AT5G66170           8.897769                 8.360052                 9.742330
## AT1G56300           7.523144                 8.848454                 9.219751
## AT1G51420           8.195223                 9.016304                 9.233940
## AT5G01210           7.185841                 9.479646                 9.318483
## AT3G21510           8.998282                 7.943693                 8.077695
## AT5G66780           5.300100                 4.882391                 5.499865
## AT3G22121           8.590686                 7.879061                 8.869064
## AT5G07010           7.289225                 8.275836                 8.960074
## AT5G41280           9.221440                 8.229455                 7.505974
## AT5G13330           8.219223                 8.385657                 8.482108
## AT1G49720           8.252166                 8.439622                 9.013144
## AT3G22120           8.619827                 7.760114                 8.536545
## AT2G46680           6.998847                 8.215245                 8.174054
## AT5G15120           7.243148                 8.252832                 7.417571
## AT3G53160           6.419795                 7.448069                 7.794668
## AT2G18690           6.452559                 6.805586                 7.498157
## AT2G15960           6.998847                 5.927733                 7.940229
## AT3G17790           7.777065                 7.511467                 7.632756
## AT4G13195           6.334472                 7.623314                 7.768914
## AT5G02810           7.402560                 7.848697                 8.441927
## AT4G13390           5.784828                 5.466086                 7.574479
## AT2G44080           7.648631                 7.439945                 7.762402
## AT1G12040           6.531356                 5.400615                 6.756338
## AT1G22770           7.156310                 8.038210                 7.788273
## AT4G33070           7.270970                 7.836371                 7.409260
## AT3G52770           6.021603                 4.833612                 5.648505
## AT4G33980           7.053267                 7.142413                 7.366967
## AT2G43570           4.623494                 6.512082                 6.544984
## AT2G36470           5.908068                 7.112056                 7.857113
## AT1G06460           4.885877                 6.542753                 7.425836
## AT1G48930           6.871366                 5.806588                 5.906481
## AT5G48175           6.186502                 7.049356                 7.278470
## AT5G02230           5.226228                 4.783127                 5.402726
## AT1G11210           5.263637                 6.572785                 7.314523
## AT4G12290           6.452559                 6.415951                 7.030096
## AT5G18470           5.335664                 4.369446                 6.589805
## AT3G23150           6.186502                 6.727640                 6.702935
## AT5G57540           4.734235                 3.566154                 5.619977
## AT5G24470           6.846927                 6.915138                 6.529729
## AT5G61650           5.884248                 5.296478                 7.072823
## AT1G02450           5.437381                 5.701770                 5.648505
## AT5G19790           5.678047                 3.886187                 6.084069
## AT2G28690           5.784828                 6.645240                 4.931600
## AT2G05520           2.317106                 6.330640                 6.450937
## AT2G20520           2.000000                 2.000000                 5.676480
## AT5G42900           6.546612                 5.400615                 5.435838
## AT1G54970           4.503539                 3.305011                 5.676480
## AT5G22270           5.592433                 5.433722                 6.845286
## AT2G20560           5.066066                 5.184234                 5.975663
## AT1G28480           3.981833                 2.575589                 4.678492
## AT3G53800           6.419795                 5.950788                 6.104806
## AT5G61660           5.370373                 4.882391                 6.647478
## AT5G18270           5.621539                 5.466086                 5.676480
## AT3G10040           5.592433                 6.039489                 6.063029
## AT4G03440           6.262383                 5.995820                 5.298572
## AT3G04070           4.623494                 4.369446                 5.703923
## AT3G10710           3.307413                 3.886187                 4.149763
## AT1G79320           3.790058                 3.680902                 3.442957
## AT1G64480           5.226228                 4.225627                 5.368837
## AT3G05930           4.933077                 5.260025                 4.371327
## AT1G01660           4.068937                 4.147957                 3.567698
## AT5G25190           4.734235                 5.019549                 4.622069
## AT4G35180           4.734235                 3.154268                 3.980563
## AT1G16440           2.987914                 3.154268                 3.682507
## AT2G46860           3.981833                 2.575589                 2.000000
## AT1G25240           2.000000                 2.000000                 4.502139
## AT1G79860           3.790058                 2.316311                 2.576356
##           Col0PhyD_FLT_Alight_Rep3
## AT3G62040                 6.510881
## AT5G05960                 6.699485
## AT5G13930                 2.000000
## AT2G21640                 3.977886
## AT4G31910                 8.160672
## AT3G03780                 6.878324
## AT2G40900                 6.346916
## AT2G41480                 6.398092
## AT5G63850                 7.293113
## AT3G54500                 6.080693
## AT3G02850                 5.830478
## AT5G37260                 6.142022
## AT4G31730                 5.221506
## AT3G23810                 6.431227
## AT3G17609                 3.565322
## AT3G26830                 4.224640
## AT5G05270                 4.832533
## AT2G46830                 2.575176
## AT3G51240                 2.985295
## AT3G09600                 4.619065
## AT5G17300                 4.974167
## AT5G47990                 2.000000
## AT4G01440                 4.298327
## AT4G09950                 6.541551
## AT1G78580                 4.619065
## AT5G50120                 4.146985
## AT3G54820                 2.000000
## AT5G44350                 4.146985
## AT2G47560                 2.316064
## AT3G57020                 2.575176
## AT3G06020                 2.000000
## AT5G08640                 2.000000
## AT3G03770                 4.560370
## AT2G25680                 2.794760
## AT1G30380                 4.064912
## AT3G56730                 3.153577
## AT5G56720                 4.435290
## AT5G64940                 2.316064
## AT2G47460                 2.316064
## AT2G02020                 2.575176
## AT5G50800                 2.000000
## AT4G24670                 4.499185
## AT1G29910                 3.153577
## AT1G11700                 2.575176
## AT4G25830                 2.316064
## AT4G15430                 3.153577
## AT4G26790                 3.977886
## AT1G68585                 2.575176
## AT5G13630                 2.794760
## AT1G62710                 2.794760
## AT3G05880                12.809855
## AT3G44300                12.211254
## AT2G26400                 9.020512
## AT3G54040                 9.887934
## AT1G19960                10.129153
## AT5G23220                 9.779536
## AT5G24530                 9.946405
## AT5G22555                 9.143073
## AT3G56400                 9.438213
## AT5G05500                 8.660726
## AT5G66170                 9.750294
## AT1G56300                 9.039439
## AT1G51420                 8.947955
## AT5G01210                 7.636363
## AT3G21510                 9.127994
## AT5G66780                 4.729744
## AT3G22121                 8.228217
## AT5G07010                 8.237613
## AT5G41280                 7.998802
## AT5G13330                 9.031358
## AT1G49720                 8.705428
## AT3G22120                 8.063633
## AT2G46680                 7.058779
## AT5G15120                 8.185160
## AT3G53160                 7.930920
## AT2G18690                 7.692104
## AT2G15960                 8.712184
## AT3G17790                 7.284072
## AT4G13195                 7.470944
## AT5G02810                 8.068906
## AT4G13390                 5.464944
## AT2G44080                 7.161081
## AT1G12040                 7.346197
## AT1G22770                 7.877827
## AT4G33070                 6.495298
## AT3G52770                 5.527567
## AT4G33980                 7.841313
## AT2G43570                 6.161898
## AT2G36470                 7.865758
## AT1G06460                 7.901665
## AT1G48930                 6.541551
## AT5G48175                 6.925598
## AT5G02230                 5.994643
## AT1G11210                 7.363467
## AT4G12290                 6.960063
## AT5G18470                 7.685253
## AT3G23150                 7.110837
## AT5G57540                 2.000000
## AT5G24470                 5.496595
## AT5G61650                 4.298327
## AT1G02450                 4.499185
## AT5G19790                 5.018448
## AT2G28690                 6.526298
## AT2G05520                 6.080693
## AT2G20520                 2.000000
## AT5G42900                 5.805423
## AT1G54970                 2.794760
## AT5G22270                 5.399479
## AT2G20560                 6.902155
## AT1G28480                 3.304264
## AT3G53800                 6.238776
## AT5G61660                 3.786301
## AT5G18270                 4.928483
## AT3G10040                 5.221506
## AT4G03440                 6.059657
## AT3G04070                 5.830478
## AT3G10710                 4.560370
## AT1G79320                 4.064912
## AT1G64480                 5.143678
## AT3G05930                 5.903133
## AT1G01660                 3.786301
## AT5G25190                 5.753969
## AT4G35180                 4.224640
## AT1G16440                 3.565322
## AT2G46860                 2.575176
## AT1G25240                 2.316064
## AT1G79860                 2.985295
## 
## $bar
## AT3G62040 AT5G05960 AT5G13930 AT2G21640 AT4G31910 AT3G03780 AT2G40900 AT2G41480 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT5G63850 AT3G54500 AT3G02850 AT5G37260 AT4G31730 AT3G23810 AT3G17609 AT3G26830 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT5G05270 AT2G46830 AT3G51240 AT3G09600 AT5G17300 AT5G47990 AT4G01440 AT4G09950 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT1G78580 AT5G50120 AT3G54820 AT5G44350 AT2G47560 AT3G57020 AT3G06020 AT5G08640 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT3G03770 AT2G25680 AT1G30380 AT3G56730 AT5G56720 AT5G64940 AT2G47460 AT2G02020 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT5G50800 AT4G24670 AT1G29910 AT1G11700 AT4G25830 AT4G15430 AT4G26790 AT1G68585 
##        -1        -1        -1        -1        -1        -1        -1        -1 
## AT5G13630 AT1G62710 AT3G05880 AT3G44300 AT2G26400 AT3G54040 AT1G19960 AT5G23220 
##        -1        -1         1         1         1         1         1         1 
## AT5G24530 AT5G22555 AT3G56400 AT5G05500 AT5G66170 AT1G56300 AT1G51420 AT5G01210 
##         1         1         1         1         1         1         1         1 
## AT3G21510 AT5G66780 AT3G22121 AT5G07010 AT5G41280 AT5G13330 AT1G49720 AT3G22120 
##         1         1         1         1         1         1         1         1 
## AT2G46680 AT5G15120 AT3G53160 AT2G18690 AT2G15960 AT3G17790 AT4G13195 AT5G02810 
##         1         1         1         1         1         1         1         1 
## AT4G13390 AT2G44080 AT1G12040 AT1G22770 AT4G33070 AT3G52770 AT4G33980 AT2G43570 
##         1         1         1         1         1         1         1         1 
## AT2G36470 AT1G06460 AT1G48930 AT5G48175 AT5G02230 AT1G11210 AT4G12290 AT5G18470 
##         1         1         1         1         1         1         1         1 
## AT3G23150 AT5G57540 AT5G24470 AT5G61650 AT1G02450 AT5G19790 AT2G28690 AT2G05520 
##         1         1         1         1         1         1         1         1 
## AT2G20520 AT5G42900 AT1G54970 AT5G22270 AT2G20560 AT1G28480 AT3G53800 AT5G61660 
##         1         1         1         1         1         1         1         1 
## AT5G18270 AT3G10040 AT4G03440 AT3G04070 AT3G10710 AT1G79320 AT1G64480 AT3G05930 
##         1         1         1         1         1         1         1         1 
## AT1G01660 AT5G25190 AT4G35180 AT1G16440 AT2G46860 AT1G25240 AT1G79860 
##         1         1         1         1         1         1         1

 # Save gene lists and data into files
 write.csv( selectedHeatmap.data()$genes, 'heatmap.data.csv') 
 write.csv(DEG.data(),'DEG.data.csv' )
 write(AllGeneListsGMT() ,'AllGeneListsGMT.gmt')
 input_selectGO2 <- 'GOBP'  #Gene set category 
 geneListData.out <- geneListData()  
 volcanoPlot()  

  scatterPlot()  

  MAplot()  

  geneListGOTable.out <- geneListGOTable()  
 # Read pathway data again 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO2,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  ) 
 input_removeRedudantSets <- TRUE   #Remove highly redundant gene sets? 
 results <- geneListGO()  #Enrichment analysis
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Direction adj.Pval nGenes Pathways
Down regulated 3.2e-06 6 Flavonoid metabolic process
1.4e-05 16 Response to abiotic stimulus
1.4e-05 5 Flavonoid biosynthetic process
1.6e-05 6 Circadian rhythm
1.6e-05 8 Response to auxin
1.9e-05 6 Rhythmic process
1.5e-04 9 Response to light stimulus
1.8e-04 9 Response to radiation
5.3e-04 3 Neutral amino acid transport
5.8e-04 4 Response to UV-B
Up regulated 2.0e-06 9 Phosphorelay signal transduction system
5.4e-06 20 Response to organic substance
7.0e-06 18 Response to endogenous stimulus
7.0e-06 18 Response to hormone
1.7e-05 17 Response to oxygen-containing compound
2.0e-05 9 Response to organic cyclic compound
8.9e-05 8 Response to antibiotic
1.4e-04 16 System development
1.6e-04 10 Intracellular signal transduction
1.6e-04 15 Cellular response to chemical stimulus

STRING-db API access. We need to find the taxonomy id of your species, this used by STRING. First we try to guess the ID based on iDEP’s database. Users can also skip this step and assign NCBI taxonomy id directly by findTaxonomyID.out = 10090 # mouse 10090, human 9606 etc.

 STRING10_species = read.csv(STRING10_speciesFile)  
 ix = grep('Arabidopsis thaliana', STRING10_species$official_name ) 
 findTaxonomyID.out <- STRING10_species[ix,1] # find taxonomyID
 findTaxonomyID.out  
## [1] 3702

Enrichment analysis using STRING

  STRINGdb_geneList.out <- STRINGdb_geneList() #convert gene lists
## Warning:  we couldn't map to STRING 0% of your identifiers
 input_STRINGdbGO <- 'Process'  #'Process', 'Component', 'Function', 'KEGG', 'Pfam', 'InterPro' 
 results <- stringDB_GO_enrichmentData()  # enrichment using STRING 
## Warning in string_db$get_enrichment(ids, category = input_STRINGdbGO, methodMT =
## "fdr", : methodMT parameter is depecated. Only FDR correction is available.
## Warning in string_db$get_enrichment(ids, category = input_STRINGdbGO, methodMT =
## "fdr", : iea parameter is deprecated.
## [1] "Process"
## Warning in string_db$get_enrichment(ids, category = input_STRINGdbGO, methodMT =
## "fdr", : methodMT parameter is depecated. Only FDR correction is available.

## Warning in string_db$get_enrichment(ids, category = input_STRINGdbGO, methodMT =
## "fdr", : iea parameter is deprecated.
## [1] "Process"
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
“No significant enrichment found.” adj.Pval
No significant enrichment found. NULL

PPI network retrieval and analysis

 input_nGenesPPI <- 100 #Number of top genes for PPI retrieval and analysis 
 stringDB_network1(1) #Show PPI network 

Generating interactive PPI

 write(stringDB_network_link(), 'PPI_results.html') # write results to html file 
## Warning: 'string_db$get_link' is deprecated.
## Use 'Contact developers to request functionality' instead.
## See help("Deprecated")
## Warning:  we couldn't map to STRING 0% of your identifiers
## Warning: 'string_db$get_link' is deprecated.
## Use 'Contact developers to request functionality' instead.
## See help("Deprecated")

## Warning: 'string_db$get_link' is deprecated.
## Use 'Contact developers to request functionality' instead.
## See help("Deprecated")
 browseURL('PPI_results.html') # open in browser 

8. Pathway analysis

 input_selectContrast1 <- 'Microgravity-Terrestrial'    #select Comparison 
 #input_selectContrast1 = limma.out$comparisons[3] # manually set
 input_selectGO <- 'GOBP'   #Gene set category 
 #input_selectGO='custom' # if custom gmt file
 input_minSetSize <- 15 #Min size for gene set
 input_maxSetSize <- 2000   #Max size for gene set 
 # Read pathway data again 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  ) 
 input_pathwayPvalCutoff <- 0.2 #FDR cutoff
 input_nPathwayShow <- 30   #Top pathways to show
 input_absoluteFold <- FALSE    #Use absolute values of fold-change?
 input_GenePvalCutoff <- 1  #FDR to remove genes 

 input_pathwayMethod = 1  # 1  GAGE
 gagePathwayData.out <- gagePathwayData()  # pathway analysis using GAGE  
   
 results <- gagePathwayData.out  #Enrichment analysis for k-Means clusters  
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Direction GAGE analysis: Microgravity vs Terrestrial statistic Genes adj.Pval
Down Photosynthesis -5.401 223 1.1e-04
Ribonucleoprotein complex biogenesis -5.01 438 3.5e-04
RNA modification -4.8591 321 4.9e-04
Ribosome biogenesis -4.734 343 7.0e-04
NcRNA metabolic process -4.2086 425 5.6e-03
NcRNA processing -4.1143 357 7.2e-03
Cellular response to DNA damage stimulus -3.7807 337 2.3e-02
RRNA processing -3.7162 239 2.5e-02
DNA repair -3.7091 314 2.5e-02
RRNA metabolic process -3.6563 244 2.8e-02
Up Cellular response to decreased oxygen levels 7.4246 176 3.4e-10
Cellular response to oxygen levels 7.4246 176 3.4e-10
Cellular response to hypoxia 7.3912 175 3.4e-10
Response to hypoxia 7.0149 197 1.8e-09
Response to oxygen levels 6.991 201 1.8e-09
Response to decreased oxygen levels 6.9904 200 1.8e-09
Root epidermal cell differentiation 4.1893 115 5.4e-03
Plant epidermal cell differentiation 4.0288 132 7.7e-03
Response to toxic substance 4.0187 275 7.7e-03
Trichoblast differentiation 3.938 102 1.1e-02
Cell maturation 3.6762 96 2.2e-02
Trichoblast maturation 3.6762 96 2.2e-02
Root hair cell differentiation 3.6762 96 2.2e-02
Anatomical structure maturation 3.5015 151 3.2e-02
Response to antibiotic 3.4886 255 3.2e-02
Antibiotic metabolic process 3.4875 188 3.2e-02
Antibiotic catabolic process 3.455 78 3.8e-02
Response to drug 3.4042 482 3.8e-02
Cellular response to toxic substance 3.3863 148 3.8e-02
Response to reactive oxygen species 3.3836 145 3.8e-02
 pathwayListData.out = pathwayListData() 
 enrichmentPlot(pathwayListData.out, 25  ) 

  enrichmentNetwork(pathwayListData.out )  

  enrichmentNetworkPlotly(pathwayListData.out) 

## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
 input_pathwayMethod = 3  # 1  fgsea 
 fgseaPathwayData.out <- fgseaPathwayData() #Pathway analysis using fgsea 
## Warning in fgsea(pathways = gmt, stats = fold, minSize = input_minSetSize, :
## You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To
## run fgseaMultilevel, you need to remove the nperm argument in the fgsea function
## call.
 results <- fgseaPathwayData.out  #Enrichment analysis for k-Means clusters 
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
Direction GSEA analysis: Microgravity vs Terrestrial NES Genes adj.Pval
Down Photosynthesis -2.3258 223 6.5e-03
Flavonoid metabolic process -2.3107 68 6.5e-03
Response to UV-B -2.2799 59 6.5e-03
Flavonoid biosynthetic process -2.2798 50 6.5e-03
Response to UV -2.1905 95 6.5e-03
Regulation of flavonoid biosynthetic process -2.1518 16 6.5e-03
Regulation of anthocyanin metabolic process -2.0566 19 6.5e-03
Response to gravity -2.0493 78 1.0e-02
Photosynthesis, light reaction -2.011 119 6.5e-03
Anthocyanin-containing compound biosynthetic process -1.9906 20 1.4e-02
Anthocyanin-containing compound metabolic process -1.9898 35 1.4e-02
Regulation of response to red or far red light -1.9835 34 1.6e-02
Response to far red light -1.9802 45 1.0e-02
Response to red light -1.9735 55 1.6e-02
Up Cellular response to decreased oxygen levels 2.4397 176 6.5e-03
Cellular response to oxygen levels 2.4397 176 6.5e-03
Cellular response to hypoxia 2.4371 175 6.5e-03
Response to hypoxia 2.3544 197 6.5e-03
Response to decreased oxygen levels 2.3491 200 6.5e-03
Response to oxygen levels 2.3466 201 6.5e-03
Root epidermal cell differentiation 2.2177 115 6.5e-03
Trichoblast differentiation 2.2171 102 6.5e-03
Plant epidermal cell differentiation 2.1658 132 6.5e-03
Cell maturation 2.1644 96 6.5e-03
Trichoblast maturation 2.1644 96 6.5e-03
Root hair cell differentiation 2.1644 96 6.5e-03
Root hair cell development 2.1025 78 6.5e-03
Root hair elongation 2.0496 58 6.5e-03
Response to hydrogen peroxide 2.0103 65 6.5e-03
Indole glucosinolate metabolic process 1.9891 27 9.8e-03
  pathwayListData.out = pathwayListData() 
 enrichmentPlot(pathwayListData.out, 25  ) 

  enrichmentNetwork(pathwayListData.out )  

  enrichmentNetworkPlotly(pathwayListData.out) 

   PGSEAplot() # pathway analysis using PGSEA 
## 
## Computing P values using ANOVA

9. Chromosome

 input_selectContrast2 <- 'Terrestrial-Microgravity'    #select Comparison 
 #input_selectContrast2 = limma.out$comparisons[3] # manually set
 input_limmaPvalViz <- 0.1  #FDR to filter genes
 input_limmaFCViz <- 2  #FDR to filter genes 
 genomePlotly() # shows fold-changes on the genome 
## Warning in eval(quote(list(...)), env): NAs introduced by coercion
## Warning in genomePlotly(): NAs introduced by coercion

10. Biclustering

 input_nGenesBiclust <- 1000    #Top genes for biclustering
 input_biclustMethod <- 'BCCC()'    #Method: 'BCCC', 'QUBIC', 'runibic' ... 
 biclustering.out = biclustering()  # run analysis

 input_selectBicluster <- 1 #select a cluster 
 biclustHeatmap()   # heatmap for selected cluster 

 input_selectGO4 <- 'GOBP'  #Gene set category 
 # Read pathway data again 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO4,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  )  
 results <- geneListBclustGO()  #Enrichment analysis for k-Means clusters   
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
adj.Pval Genes Pathways
1.9e-120 192 Peptide metabolic process
1.9e-117 182 Translation
3.3e-117 182 Peptide biosynthetic process
8.8e-113 185 Amide biosynthetic process
2.1e-111 196 Cellular amide metabolic process
5.5e-96 238 Organonitrogen compound biosynthetic process
1.4e-68 151 Response to inorganic substance
6.0e-57 101 Response to metal ion
1.3e-53 86 Response to cadmium ion
4.4e-49 197 Response to abiotic stimulus

11. Co-expression network

 input_mySoftPower <- 5 #SoftPower to cutoff
 input_nGenesNetwork <- 1000    #Number of top genes
 input_minModuleSize <- 20  #Module size minimum 
 wgcna.out = wgcna()   # run WGCNA  
## Warning: executing %dopar% sequentially: no parallel backend registered
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.7780  1.540          0.918  368.00    378.00  520.0
## 2      2   0.2370  0.285          0.681  189.00    190.00  333.0
## 3      3   0.0936 -0.126          0.651  114.00    108.00  234.0
## 4      4   0.5360 -0.387          0.797   74.60     67.20  176.0
## 5      5   0.7270 -0.553          0.905   52.10     44.20  140.0
## 6      6   0.8430 -0.724          0.971   38.10     30.50  116.0
## 7      7   0.8550 -0.824          0.955   28.80     21.40   98.1
## 8      8   0.9000 -0.922          0.984   22.40     15.90   84.7
## 9      9   0.9090 -0.995          0.969   17.80     12.00   74.2
## 10    10   0.9080 -1.060          0.953   14.40      9.25   65.6
## 11    12   0.9290 -1.130          0.950    9.86      5.67   52.5
## 12    14   0.9370 -1.180          0.941    7.06      3.53   43.0
## 13    16   0.9550 -1.210          0.949    5.24      2.34   35.8
## 14    18   0.9530 -1.220          0.940    4.00      1.54   30.2
## 15    20   0.9730 -1.230          0.965    3.12      1.08   25.8
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
 softPower()  # soft power curve 

  modulePlot()  # plot modules  

  listWGCNA.Modules.out = listWGCNA.Modules() #modules
 input_selectGO5 <- 'GOBP'  #Gene set category 
 # Read pathway data again 
 GeneSets.out <-readGeneSets( geneSetFile,
    convertedData.out, input_selectGO5,input_selectOrg,
    c(input_minSetSize, input_maxSetSize)  ) 
 input_selectWGCNA.Module <- 'Entire network'   #Select a module
 input_topGenesNetwork <- 10    #SoftPower to cutoff
 input_edgeThreshold <- 0.4 #Number of top genes 
 moduleNetwork()    # show network of top genes in selected module
##  softConnectivity: FYI: connecitivty of genes with less than 12 valid samples will be returned as NA.
##  ..calculating connectivities..

 input_removeRedudantSets <- TRUE   #Remove redundant gene sets 
 results <- networkModuleGO()  #Enrichment analysis of selected module
 results$adj.Pval <- format( results$adj.Pval,digits=3 )
 kable( results, row.names=FALSE) %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  scroll_box(width = "100%") 
adj.Pval Genes Pathways
1.9e-120 192 Peptide metabolic process
1.9e-117 182 Translation
3.3e-117 182 Peptide biosynthetic process
8.8e-113 185 Amide biosynthetic process
2.1e-111 196 Cellular amide metabolic process
5.5e-96 238 Organonitrogen compound biosynthetic process
1.4e-68 151 Response to inorganic substance
6.0e-57 101 Response to metal ion
1.3e-53 86 Response to cadmium ion
4.4e-49 197 Response to abiotic stimulus